FSL warp to ANTs (nii.gz to .h5)

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1

Dear all,

I have some transformations calculated using a combination of FSL and ANTs. They have been merged into one final warp interpretable to FSL (using wb_command -convert-warpfield). This transformation contains some warps and affine transformations. I would like to convert it to itk (ants interpretable), .h5 to be more precise. Is there any possibility to do this? Thanks in advance.

Best regards,

Manuel

2

Hi,

c3d may be your friend there. I never tried myself for warps, I know it works well for affine transforms.

This discussion may be of interest for you:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;c21935f9.1901

Let us know if you find a solution that works for you! Thanks!

Julien

3

Hi Manuel,

I am having the same issue here. I am trying to convert a warpfield generated by FNIRT to a ANTs readable format (as you suggested, .h5 file could be a way to go), but using wb_command -convert-warpfield -from-fnirt {input} {source} -to-itk {output} generates a .nii.gz file, which ANTs is not able to recognise.

In my case I am using the antsApplyTransforms command, where I would like to include the file I am trying to convert as a --transform file to perform a registration. The following exception is raised:

Transform reader for {path_to_file}/non-linear_warp-coeffs_postt1w_to_pret1w_ants_format.nii.gz caught an ITK exception:

itk::ExceptionObject (0x5f0bab1ac440)
Location: "unknown" 
File: /home/runner/work/_temp/build/ITKv5/Modules/IO/TransformBase/src/itkTransformFileReader.cxx
Line: 128
Description: ITK ERROR: TransformFileReaderTemplate(0x5f0bab1c5790): Could not create Transform IO object for reading file {path_to_file}/non-linear_warp-coeffs_postt1w_to_pret1w_ants_format.nii.gz
  Tried to create one of the following:
    HDF5TransformIOTemplate
    HDF5TransformIOTemplate
    MINCTransformIOTemplate
    MINCTransformIOTemplate
    MatlabTransformIOTemplate
    MatlabTransformIOTemplate
    TxtTransformIOTemplate
    TxtTransformIOTemplate
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

I have found that the c3d_affine_tool is useful in certain cases similar to this one, but as these warpfields refer to non-linear transformations, affine matrices are not the way to go here.

I am not able to use ConvertTransformFile either, as there is no way that ANTs understands this .nii.gz file that the Connectome Workbench is giving me as an output. I am reviving this topic as it was very difficult for me to find another ongoing thread here or elsewhere dealing with this same issue. I hope you can remember/recollect any useful information/scripts that you were using at that time and give me a hand :). Thank you in advance,

Doneka